"The experiment, which also involved using ground stations to take measurements of the ionosphere, was intended to develop scientific explanations for ionospheric disturbances and their effects on modern technology, officials said."

This has all been done before[2] as it turns out! In 1956 the Air Force launched two missiles from White Sands Missile Range with payloads of nitric oxide. The gas released in the ionosphere created a glowing cloud described as being 'yellow-red'[3] in color. They were studying the ionosphere as well, which, back in 1958, was described with a bit more panache [4]:

"In this electronic age, everybody knows that the ionosphere is an electrified upper atmosphere region that bounces off radio waves around the globe."

The 1958 definition of the ionosphere also nicely explains what the experiment in both cases was looking for: how radio wave propagation was effected, (also shown in the following diagram from the same 1958 piece):

The folks at Mysterious Universe[5] seem a little peeved about the DoD's failure to reveal what the specific released vapor was, but while the vapor could have been a number of things, it's interesting to note the color of light emitted by ionized nitrogen: